The invention discloses a 3D terrain imaging system of the interferometric synthetic aperture radar (InSAR) and an elevation mapping method thereof, which mainly solve the problems that the existing InSAR has bad imaging pragmaticality and can not implement 3D elevation mapping on the fast-changing terrain and the transilient terrain. The system comprises three sub-aperture antennas, a radar transmitter, a radar receiver and an imaging data processor; the imaging signal processor comprises a SAR image processing unit and an InSAR image processing unit. The invention receives radar echo through the three sub-apertures, then conducts SAR imaging process on the radar echo respectively received by the three sub-apertures, and then conducts InSAR imaging process on the obtained SAR complex pattern, wherein the InSAR imaging process comprises image registration, phase filtering and phase unfolding based on cluster analysis. The processed InSAR phase unfolded image is processed with an elevation inversion to recover a three dimensional digital elevation map. The invention has the advantages of wide adaptability to mapped terrains, and high imaging effectiveness, therefore, the invention can be used in the mapping of the 3D terrain.